File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 73504ms, 86.61% of 84871ms total Dropped 890 nodes (cum <= 424.36ms) flat flat% sum% cum cum% 0 0% 0% 84804ms 99.92% __libc_start_call_main 0 0% 0% 84804ms 99.92% __libc_start_main_impl 0 0% 0% 84804ms 99.92% _start 0 0% 0% 84786ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 84786ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 84786ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 84786ms 99.90% main 0 0% 0% 84741ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 84741ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 84740ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 84411ms 99.46% AbstractCellBasedSimulation::Solve 0 0% 0% 73001ms 86.01% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 72945ms 85.95% MeshBasedCellPopulation::Update 0 0% 0% 45478ms 53.58% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 45476ms 53.58% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 409ms 0.48% 0.48% 39042ms 46.00% VertexMesh::VertexMesh 0 0% 0.48% 22317ms 26.30% MutableMesh::ReMesh 0 0% 0.48% 16323ms 19.23% tetgen::tetrahedralize 631ms 0.74% 1.23% 16304ms 19.21% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0012% 1.23% 16175ms 19.06% tetgen::tetgenmesh::delaunizevertices 14ms 0.016% 1.24% 16166ms 19.05% tetgen::tetgenmesh::incrflipdelaunay 516ms 0.61% 1.85% 14407ms 16.98% tetgen::tetgenmesh::lawson 28ms 0.033% 1.88% 13975ms 16.47% std::set::insert (inline) 222ms 0.26% 2.15% 13510ms 15.92% std::_Rb_tree::_M_insert_unique 611ms 0.72% 2.87% 12408ms 14.62% VertexElement::AddFace 3207ms 3.78% 6.64% 11700ms 13.79% std::_Rb_tree::_M_lower_bound (inline) 241ms 0.28% 6.93% 10763ms 12.68% std::_Rb_tree::find (inline) 0 0% 6.93% 10178ms 11.99% std::set::count (inline) 9755ms 11.49% 18.42% 9755ms 11.49% std::_Rb_tree_increment 182ms 0.21% 18.64% 8474ms 9.98% operator new 1240ms 1.46% 20.10% 8184ms 9.64% __GI___libc_malloc 3ms 0.0035% 20.10% 8059ms 9.50% std::set_intersection (inline) 379ms 0.45% 20.55% 8056ms 9.49% std::__set_intersection 336ms 0.4% 20.94% 7967ms 9.39% std::_Rb_tree::_M_insert_ (inline) 98ms 0.12% 21.06% 7909ms 9.32% std::less::operator() (inline) 7872ms 9.28% 30.33% 7872ms 9.28% std::operator< (inline) 191ms 0.23% 30.56% 7118ms 8.39% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 30.56% 6731ms 7.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 46ms 0.054% 30.61% 6681ms 7.87% std::__new_allocator::allocate (inline) 0 0% 30.61% 6657ms 7.84% std::allocator_traits::allocate (inline) 0 0% 30.61% 6535ms 7.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 4777ms 5.63% 36.24% 6526ms 7.69% _int_malloc 8ms 0.0094% 36.25% 6514ms 7.68% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 36.25% 6490ms 7.65% VertexMesh::~VertexMesh 63ms 0.074% 36.33% 6461ms 7.61% Node::AddElement 1538ms 1.81% 38.14% 6235ms 7.35% __GI___libc_free 0 0% 38.14% 5940ms 7.00% std::_Rb_tree::~_Rb_tree (inline) 2328ms 2.74% 40.88% 5937ms 7.00% std::_Rb_tree::_M_erase 0 0% 40.88% 5870ms 6.92% std::set::~set (inline) 5680ms 6.69% 47.57% 5680ms 6.69% std::_Rb_tree::_S_right (inline) 1379ms 1.62% 49.20% 5607ms 6.61% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 49.20% 5548ms 6.54% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.0094% 49.21% 5468ms 6.44% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 129ms 0.15% 49.36% 5461ms 6.43% std::__new_allocator::deallocate (inline) 0 0% 49.36% 5445ms 6.42% std::allocator_traits::deallocate (inline) 0 0% 49.36% 5369ms 6.33% std::_Rb_tree::_M_create_node (inline) 18ms 0.021% 49.38% 5342ms 6.29% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 49.38% 5324ms 6.27% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 49.38% 5312ms 6.26% std::_Rb_tree::_M_get_node (inline) 75ms 0.088% 49.47% 4839ms 5.70% MutableElement::AddNode 11ms 0.013% 49.48% 4776ms 5.63% TetrahedralMesh::ImportFromMesher 1455ms 1.71% 51.20% 4690ms 5.53% _int_free 0 0% 51.20% 4482ms 5.28% AbstractCellPopulation::WriteResultsToFiles 293ms 0.35% 51.54% 3975ms 4.68% Node::~Node 111ms 0.13% 51.67% 3844ms 4.53% tetgen::tetgenmesh::insphere_sos 222ms 0.26% 51.93% 3740ms 4.41% VertexMesh::Clear 3424ms 4.03% 55.97% 3715ms 4.38% tetgen::insphere 137ms 0.16% 56.13% 3589ms 4.23% tetgen::tetgenmesh::flip23 3412ms 4.02% 60.15% 3412ms 4.02% Node::GetIndex 2322ms 2.74% 62.89% 3305ms 3.89% malloc_consolidate 190ms 0.22% 63.11% 3118ms 3.67% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 48ms 0.057% 63.17% 3090ms 3.64% std::_Vector_base::_M_deallocate (inline) 6ms 0.0071% 63.17% 3043ms 3.59% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0012% 63.17% 2973ms 3.50% std::_Rb_tree_iterator::operator++ (inline) 0 0% 63.17% 2960ms 3.49% std::vector::~vector (inline) 0 0% 63.17% 2922ms 3.44% std::_Vector_base::~_Vector_base (inline) 7ms 0.0082% 63.18% 2914ms 3.43% _int_free_maybe_consolidate 8ms 0.0094% 63.19% 2556ms 3.01% Element::Element 118ms 0.14% 63.33% 2534ms 2.99% tetgen::tetgenmesh::flip32 2432ms 2.87% 66.20% 2432ms 2.87% std::_Rb_tree_insert_and_rebalance 0 0% 66.20% 2415ms 2.85% std::_Rb_tree::_M_drop_node (inline) 0 0% 66.20% 2403ms 2.83% std::_Rb_tree::_M_put_node (inline) 2258ms 2.66% 68.86% 2258ms 2.66% unlink_chunk 11ms 0.013% 68.87% 2178ms 2.57% Element::RegisterWithNodes (inline) 10ms 0.012% 68.88% 2083ms 2.45% VertexMesh::GenerateVerticesFromElementCircumcentres 245ms 0.29% 69.17% 2026ms 2.39% tetgen::tetgenmesh::enqueueflipface 101ms 0.12% 69.29% 1701ms 2.00% TetrahedralMesh::Clear 1542ms 1.82% 71.11% 1617ms 1.91% tetgen::orient3d 71ms 0.084% 71.19% 1545ms 1.82% std::map::operator[] 1329ms 1.57% 72.76% 1540ms 1.81% AbstractElement::GetNodeGlobalIndex 63ms 0.074% 72.83% 1503ms 1.77% std::vector::_M_realloc_insert 57ms 0.067% 72.90% 1455ms 1.71% tetgen::tetgenmesh::locate 1407ms 1.66% 74.56% 1407ms 1.66% AbstractElement::IsDeleted 0 0% 74.56% 1356ms 1.60% std::_Rb_tree::lower_bound (inline) 0 0% 74.56% 1356ms 1.60% std::map::lower_bound (inline) 3ms 0.0035% 74.56% 1348ms 1.59% std::_Vector_base::_M_allocate (inline) 96ms 0.11% 74.67% 1338ms 1.58% tetgen::tetgenmesh::preciselocate 643ms 0.76% 75.43% 1294ms 1.52% AbstractElement::GetNodeLocation 1264ms 1.49% 76.92% 1264ms 1.49% Node::rGetLocation 133ms 0.16% 77.08% 1254ms 1.48% std::vector::push_back (inline) 0 0% 77.08% 1187ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 0 0% 77.08% 1161ms 1.37% VoronoiDataWriter::Visit 1091ms 1.29% 78.36% 1091ms 1.29% tetgen::tetgenmesh::oppo 1033ms 1.22% 79.58% 1033ms 1.22% tetgen::tetgenmesh::triface::triface 7ms 0.0082% 79.59% 942ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.02% 79.61% 919ms 1.08% AbstractTetrahedralElement::CalculateJacobian 16ms 0.019% 79.63% 891ms 1.05% Element::CalculateCircumsphere 832ms 0.98% 80.61% 832ms 0.98% [libchaste_mesh.so] 822ms 0.97% 81.57% 822ms 0.97% std::vector::size (inline) 334ms 0.39% 81.97% 811ms 0.96% tetgen::tetgenmesh::sym 1ms 0.0012% 81.97% 780ms 0.92% AbstractTwoBodyInteractionForce::AddForceContribution 53ms 0.062% 82.03% 750ms 0.88% AbstractTetrahedralElement::RefreshJacobian 13ms 0.015% 82.05% 729ms 0.86% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 699ms 0.82% 82.87% 699ms 0.82% tetgen::tetgenmesh::triface::operator= 46ms 0.054% 82.92% 662ms 0.78% tetgen::tetgenmesh::queue::push 350ms 0.41% 83.34% 653ms 0.77% tetgen::tetgenmesh::fnextself 17ms 0.02% 83.36% 622ms 0.73% boost::numeric::ublas::vector_assign (inline) 12ms 0.014% 83.37% 616ms 0.73% boost::numeric::ublas::c_vector::c_vector (inline) 364ms 0.43% 83.80% 616ms 0.73% tetgen::tetgenmesh::link::add 252ms 0.3% 84.10% 607ms 0.72% tetgen::tetgenmesh::bond 49ms 0.058% 84.15% 596ms 0.7% tetgen::tetgenmesh::enextfnext 51ms 0.06% 84.21% 584ms 0.69% __atan2 0 0% 84.21% 578ms 0.68% std::set::find (inline) 49ms 0.058% 84.27% 559ms 0.66% tetgen::tetgenmesh::enext2fnext 0 0% 84.27% 538ms 0.63% boost::numeric::ublas::inner_prod (inline) 1ms 0.0012% 84.27% 536ms 0.63% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 44ms 0.052% 84.33% 535ms 0.63% boost::numeric::ublas::vector_scalar_binary::evaluate 414ms 0.49% 84.81% 529ms 0.62% __ieee754_atan2_fma 19ms 0.022% 84.84% 508ms 0.6% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.84% 505ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 501ms 0.59% 85.43% 501ms 0.59% tetgen::tetgenmesh::decode 495ms 0.58% 86.01% 495ms 0.58% tetgen::tetgenmesh::pointmark 7ms 0.0082% 86.02% 487ms 0.57% VertexElement::~VertexElement 0 0% 86.02% 487ms 0.57% std::insert_iterator::operator= (inline) 8ms 0.0094% 86.03% 470ms 0.55% CellPropertyCollection::GetPropertiesType (inline) 460ms 0.54% 86.57% 460ms 0.54% tetgen::tetgenmesh::org 26ms 0.031% 86.60% 447ms 0.53% std::_Rb_tree_iterator::operator-- (inline) 0 0% 86.60% 432ms 0.51% std::_Rb_tree::_M_insert_unique_ (inline) 6ms 0.0071% 86.61% 427ms 0.5% Cell::GetCellId